Phylogenetic trees - Molecular evolution (Mar/23/2006 )

Hi people!
I'm not sure if this is a good place to present my problem for discussion, but anyway I will try it.
Evolutionary tree diagrams have become familiar in the literature. These trees are often presented as factual depictions of historical events. However, a more sophisticated scientific view point is that trees depict hypotheses of historical events. How a tree, viewed as hypothesis is a different interpretation than a tree viewed as a depiction of historical fact?
I'm trying to prepare myself for discussion, if somebody have good idea about this subject, I will be grateful for any suggestions. All the best!

Hi, you might be better off posting in the bioinformatic section. Of course phylogenetic trees are hypothetical, no scientific interpretation of the sort of data collected for generating trees is absolute, for example there were 2 recent papers studying the relationships of mammoths to elephants, by 2 different groups, one said that the mammoth was most closely related to the Asian elephant and the other said that the relationship was with the African elephant.

It is possible to add a time component to a phylogenetic tree if you can use and validate a molecular clock, based on a gene that is evolving at a set rate. However this is difficult to do and people argue that different genes evolve at different rates (which they do), so you cannot extrapolate from one gene to the next. Also there are arguments over the rate of evolution of a single gene anyway, so the margins of error in molecular clocks are large. It is possible to tie phylogenetic trees in with a fossil record to some extent, if there is an extensive and well dated record of the fossils.

Cheers,
Bob

Ok, so I have an example of phylogenetic tree which depicts genetic relationships between the serotypes of RNA virus based on comparison of the sequence of part of the capsid-coding region of the genome.
This dendrogram could be intrepreted as a historical fact and a hypothesis.
As far as I understand correctly, this tree considered as a depiction of historical fact provides information about the percentage difference in nucleotide sequence of different serotypes of the virus and that is all what I can consider as a fact, right?
On the other hand, if this dendrogram is interpreted as a hypothesis, one may suggest that the high mutation rate observed within capsid-coding region is due to its relevant role in determining the virus host range, or it could be concluded that some regions where this virus occured represent some factors which cause specific mutation pattern for this virus.
Do you have any other ideas about different interpretation of this tree?